1 Setup

source("helper_functions.R")
library(cytokit)
library(ggedit)
library(kableExtra)
library(monocle)
library(patchwork)
library(readxl)
library(readr)
library(R.utils)
library(Seurat)
library(tidyverse)
library(viridis)
sample <- c("joint_pons.seurat")
tables_directory <- "tables"
dir.create(tables_directory, showWarnings = FALSE)
monocle_objects_directory <- "monocle_objects"
dir.create(monocle_objects_directory, showWarnings = FALSE)

1.1 Load Seurat objects

input_directory <- "/mnt/KLEINMAN_SCRATCH/projects/sjessa/from_hydra/single_cell/2019-02_revision1/output/atlas-02"
load(file.path(input_directory, "joint_pons.seurat.Rda"))
seurat <- joint_pons
#For some reasons, there is now seurat@misc$colours and seurat@misc$colours_orig
seurat@misc$colours <- seurat@misc$colours_orig

1.2 Convert Seurat object to Monocle object.

# Convert cluster numbers to format used in levels(seurat@ident)
selected_clusters <- c(20, 13, 15, 3, 6)
selected_clusters <- paste0("^", selected_clusters, "-")
selected_clusters <- grep(paste(selected_clusters,collapse="|"), levels(seurat@ident), value=TRUE)

# Colour vector is not available in this object for these cluster IDs, so they must be recovered a saved object. seurat@misc$colours and seurat@misc$colours_orig are identical vectors. Bug will be fixed later, according to Selin.
# First, recover corresponding new cluster ID.
load("/mnt/KLEINMAN_SCRATCH/projects/sjessa/from_hydra/single_cell/2019-02_revision1/output/atlas-02/palettes_joint.Rda")
seurat@misc$colours <- pal_jp
# Cluster columns also need to be renamed.
seurat@meta.data$cluster <- as.character(seurat@meta.data$cluster_joint)

monocle <- seurat_to_monocle(seurat, selected_clusters)
#monocle <- orderCells(monocle, reverse=TRUE)
colours <- monocle@experimentData@other$colours

2 Monocle plots

2.1 Cell trajectories

p <- plot_cell_trajectory(monocle, color_by="cluster", show_branch_points=FALSE) + scale_color_manual(values=colours)
p <- p + theme(legend.title=element_blank())
show(p)

p <- p + facet_wrap(~cluster) + theme(legend.position = "none")
show(p)

plot_cell_trajectory(monocle, color_by="Pseudotime", show_branch_points = TRUE)

plot_cell_trajectory(monocle, color_by="State", show_branch_points=TRUE)

p <- plot_complex_cell_trajectory(monocle, color_by="cluster", show_branch_points=FALSE) + scale_color_manual(values=colours)
p <- p + theme(legend.title=element_blank())
show(p)

2.2 Differentially expressed genes across pseudotime

2.2.1 All genes

diff_test_res_all_genes <- differentialGeneTest(monocle,
      fullModelFormulaStr = "~sm.ns(Pseudotime)", cores=12)
sig_gene_names_all_genes <- row.names(subset(diff_test_res_all_genes, qval < 0.1))
plot_pseudotime_heatmap(monocle[sig_gene_names_all_genes,],
      cores = 12,
      num_clusters=1,
      show_rownames = FALSE)

diff_test_res_all_genes <- diff_test_res_all_genes %>% rownames_to_column("gene")
write.table(diff_test_res_all_genes, file.path(tables_directory, "2-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6_diff_test_res_all_genes.txt"), sep="\t", quote=FALSE, row.names = FALSE)

2.2.2 Transcription factors

input_directory <- "/mnt/KLEINMAN_SCRATCH/projects/blancha/analyses/njabado/single_cell/annotation/animaltfdb3.0"
input_file <- "Mus_musculus_TF.txt"
transcription_factors <- read_tsv(file.path(input_directory, input_file), col_types = cols())

2.2.2.1 Pseudotime heatmaps of significant transcription factors

2.2.2.1.1 q value < 5*10^-5
significant_genes_q_value_5_10_minus_5 <- filter(diff_test_res_all_genes, qval < 5*10^-5) %>% .$gene 
cat("Number of significant genes: ", length(significant_genes_q_value_5_10_minus_5))
## Number of significant genes:  5151
significant_transcription_factors_q_value_5_10_minus_5 <- as.character(significant_genes_q_value_5_10_minus_5[significant_genes_q_value_5_10_minus_5 %in% transcription_factors$Symbol])
cat("Number of significant transcription factors:", length(significant_transcription_factors_q_value_5_10_minus_5))
## Number of significant transcription factors: 274
plot_genes_heatmap_output_q_value_5_10_minus_5 <- plot_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_5_10_minus_5,], cluster_rows=TRUE, num_clusters=3, return_heatmap=TRUE, show_rownames = TRUE)

plot_genes_heatmap_output_q_value_5_10_minus_5 <- plot_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_5_10_minus_5,], cluster_rows=TRUE, num_clusters=1, return_heatmap=TRUE, show_rownames = TRUE)

# The RMarkdown PDF has issues, hence this custom function to save the PDF file.
save_pheatmap_pdf(plot_genes_heatmap_output_q_value_5_10_minus_5[[2]], file.path("figures", "2-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6", "diff_test_res_plots_transcription_factors_only_q_value_5_10_minus_5_heatmap_custom.pdf"), width=16, height=36)
## pdf 
##   2
heatmap_matrix_q_value_5_10_minus_5 <- plot_genes_heatmap_output_q_value_5_10_minus_5[[1]]
ph_res_q_value_5_10_minus_5 <- plot_genes_heatmap_output_q_value_5_10_minus_5[[2]]
pheatmap_ordering_q_value_5_10_minus_5 <- rownames(heatmap_matrix_q_value_5_10_minus_5[ph_res_q_value_5_10_minus_5$tree_row[["order"]],])

transcription_factors_table_q_value_5_10_minus_5 <- filter(diff_test_res_all_genes, gene %in% significant_transcription_factors_q_value_5_10_minus_5)
# Put genes from the transcription factor table in the same order
transcription_factors_table_q_value_5_10_minus_5 <- transcription_factors_table_q_value_5_10_minus_5 %>% arrange(match(gene, pheatmap_ordering_q_value_5_10_minus_5))

write.table(transcription_factors_table_q_value_5_10_minus_5, file.path(tables_directory, "2-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6-significant_transcription_factors_diff_test_analysis_qval_5_10_minus_5.txt"), sep="\t", quote=FALSE, row.names=FALSE)

heatmap_matrix_q_value_5_10_minus_5 <- plot_genes_heatmap_output_q_value_5_10_minus_5[[1]]
heatmap_matrix_q_value_5_10_minus_5 <- as.data.frame(heatmap_matrix_q_value_5_10_minus_5) %>% rownames_to_column("gene")
heatmap_matrix_q_value_5_10_minus_5 <- heatmap_matrix_q_value_5_10_minus_5 %>% arrange(match(gene, pheatmap_ordering_q_value_5_10_minus_5))
heatmap_matrix_q_value_5_10_minus_5 %>% head(20) %>% kable() %>% kable_styling() %>% scroll_box(height="200px", width="600px")
gene 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100
Rora 2.2655226 2.1976372 2.1300251 2.0626244 1.9953746 1.9282164 1.8610915 1.7939432 1.7267158 1.6593550 1.5918075 1.5240216 1.4559467 1.3875337 1.3187346 1.2495029 1.1797935 1.1095627 1.0387683 0.9673693 0.8953266 0.8226024 0.7491605 0.6749663 0.6000216 0.5244968 0.4486094 0.3725718 0.2965908 0.2208676 0.1455983 0.0709731 -0.0028230 -0.0756103 -0.1472145 -0.2174661 -0.2862006 -0.3532582 -0.4184832 -0.4817242 -0.5428335 -0.6016669 -0.6580833 -0.7119441 -0.7631132 -0.8114562 -0.8568401 -0.8991328 -0.9382024 -0.9739171 -1.0061441 -1.0347492 -1.0596114 -1.0807534 -1.0982781 -1.1122840 -1.1228651 -1.1301108 -1.1341066 -1.1349342 -1.1326717 -1.1273941 -1.1191733 -1.1080786 -1.0941767 -1.0775324 -1.0582082 -1.0362650 -1.0117619 -0.9847570 -0.9553071 -0.9234679 -0.8892945 -0.8528415 -0.8141629 -0.7733126 -0.7303444 -0.6853122 -0.6382702 -0.5892729 -0.5383755 -0.4856339 -0.4311047 -0.3748457 -0.3169156 -0.2573744 -0.1962836 -0.1337059 -0.0697059 -0.0043496 0.0622950 0.1301582 0.1991683 0.2692515 0.3403318 0.4123311 0.4851692 0.5587634 0.6330286 0.7078775
Hif3a 3.0000000 3.0000000 2.9336435 2.6986453 2.4776628 2.2702153 2.0757922 1.8938623 1.7238819 1.5653023 1.4175756 1.2801608 1.1525278 1.0341617 0.9245657 0.8232639 0.7298032 0.6437549 0.5647163 0.4923111 0.4261906 0.3660339 0.3115483 0.2624699 0.2185153 0.1792038 0.1440418 0.1125895 0.0844536 0.0592799 0.0367478 0.0165649 -0.0015370 -0.0178060 -0.0324726 -0.0457533 -0.0578520 -0.0689625 -0.0792700 -0.0889519 -0.0981797 -0.1071188 -0.1159298 -0.1247683 -0.1337850 -0.1431259 -0.1529316 -0.1633370 -0.1744705 -0.1864533 -0.1993982 -0.2134088 -0.2285682 -0.2448497 -0.2621653 -0.2804255 -0.2995401 -0.3194188 -0.3399725 -0.3611127 -0.3827530 -0.4048088 -0.4271983 -0.4498425 -0.4726653 -0.4955945 -0.5185611 -0.5415003 -0.5643511 -0.5870564 -0.6095635 -0.6318236 -0.6537921 -0.6754284 -0.6966960 -0.7175624 -0.7379985 -0.7579794 -0.7774834 -0.7964921 -0.8149906 -0.8329668 -0.8504115 -0.8673183 -0.8836829 -0.8995038 -0.9147811 -0.9295173 -0.9437163 -0.9573838 -0.9705267 -0.9831534 -0.9952731 -1.0068963 -1.0180341 -1.0286983 -1.0389015 -1.0486564 -1.0579765 -1.0668751
Ppara 2.7908849 2.6361951 2.4865194 2.3419331 2.2024874 2.0682113 1.9391147 1.8151896 1.6964129 1.5827483 1.4741479 1.3705544 1.2719029 1.1781222 1.0891367 1.0048678 0.9252352 0.8501580 0.7795566 0.7133531 0.6514729 0.5938455 0.5404057 0.4910944 0.4458174 0.4042874 0.3661794 0.3311921 0.2990457 0.2694788 0.2422467 0.2171188 0.1938772 0.1723149 0.1522347 0.1334477 0.1157724 0.0990342 0.0830639 0.0676978 0.0527767 0.0381460 0.0236551 0.0091574 -0.0054898 -0.0204253 -0.0357835 -0.0516947 -0.0682844 -0.0856731 -0.1039756 -0.1233010 -0.1437416 -0.1652873 -0.1878703 -0.2114219 -0.2358735 -0.2611563 -0.2872023 -0.3139440 -0.3413145 -0.3692484 -0.3976811 -0.4265498 -0.4557928 -0.4853505 -0.5151649 -0.5451798 -0.5753414 -0.6055975 -0.6358985 -0.6661965 -0.6964464 -0.7266050 -0.7566313 -0.7864870 -0.8161357 -0.8455435 -0.8746787 -0.9035116 -0.9320150 -0.9601637 -0.9879346 -1.0153065 -1.0422604 -1.0687791 -1.0948472 -1.1204511 -1.1455790 -1.1702206 -1.1943671 -1.2180115 -1.2411477 -1.2637715 -1.2858795 -1.3074696 -1.3285410 -1.3490936 -1.3691285 -1.3886477
Dbp 2.2506833 2.1891815 2.1281030 2.0673983 2.0070196 1.9469207 1.8870565 1.8273835 1.7678598 1.7084447 1.6490989 1.5897846 1.5304656 1.4711068 1.4116749 1.3521377 1.2924647 1.2326267 1.1725962 1.1123470 1.0518544 0.9910954 0.9300483 0.8686932 0.8070328 0.7451737 0.6832502 0.6213917 0.5597230 0.4983641 0.4374302 0.3770316 0.3172743 0.2582593 0.2000835 0.1428392 0.0866146 0.0314940 -0.0224424 -0.0751179 -0.1264593 -0.1763968 -0.2248633 -0.2717947 -0.3171295 -0.3608083 -0.4027738 -0.4429703 -0.4813437 -0.5178410 -0.5524101 -0.5849992 -0.6155648 -0.6441384 -0.6707923 -0.6955962 -0.7186165 -0.7399168 -0.7595578 -0.7775980 -0.7940931 -0.8090970 -0.8226612 -0.8348355 -0.8456677 -0.8552042 -0.8634898 -0.8705677 -0.8764801 -0.8812678 -0.8849706 -0.8876273 -0.8892760 -0.8899536 -0.8896966 -0.8885408 -0.8865214 -0.8836732 -0.8800305 -0.8756274 -0.8704975 -0.8646744 -0.8581915 -0.8510820 -0.8433792 -0.8351162 -0.8263265 -0.8170433 -0.8073002 -0.7971309 -0.7865694 -0.7756497 -0.7644063 -0.7528740 -0.7410879 -0.7290834 -0.7168963 -0.7045628 -0.6921196 -0.6796035
Nr1d1 2.3092053 2.2408024 2.1731343 2.1061427 2.0397718 1.9739678 1.9086797 1.8438586 1.7794577 1.7154328 1.6517416 1.5883440 1.5252022 1.4622803 1.3995448 1.3369640 1.2745085 1.2121508 1.1498655 1.0876292 1.0254207 0.9632207 0.9010118 0.8387788 0.7765290 0.7143707 0.6524368 0.5908536 0.5297403 0.4692096 0.4093671 0.3503124 0.2921385 0.2349323 0.1787748 0.1237415 0.0699023 0.0173224 -0.0339383 -0.0838239 -0.1322831 -0.1792682 -0.2247351 -0.2686429 -0.3109537 -0.3516319 -0.3906443 -0.4279594 -0.4635472 -0.4973791 -0.5294269 -0.5596634 -0.5880675 -0.6146823 -0.6395842 -0.6628461 -0.6845366 -0.7047210 -0.7234609 -0.7408148 -0.7568385 -0.7715848 -0.7851040 -0.7974441 -0.8086510 -0.8187686 -0.8278388 -0.8359019 -0.8429966 -0.8491602 -0.8544286 -0.8588367 -0.8624181 -0.8652054 -0.8672306 -0.8685245 -0.8691175 -0.8690393 -0.8683189 -0.8669851 -0.8650661 -0.8625898 -0.8595839 -0.8560759 -0.8520931 -0.8476627 -0.8428120 -0.8375679 -0.8319580 -0.8260094 -0.8197496 -0.8132062 -0.8064072 -0.7993805 -0.7921546 -0.7847579 -0.7772194 -0.7695683 -0.7618342 -0.7540471
Klf9 2.3396649 2.2689335 2.1988336 2.1293311 2.0603931 1.9919880 1.9240851 1.8566550 1.7896695 1.7231015 1.6569250 1.5911152 1.5256486 1.4605025 1.3956556 1.3310877 1.2667796 1.2027135 1.1388725 1.0752409 1.0118042 0.9485490 0.8854630 0.8225352 0.7597726 0.6972650 0.6351234 0.5734536 0.5123565 0.4519277 0.3922583 0.3334340 0.2755362 0.2186412 0.1628212 0.1081437 0.0546721 0.0024661 -0.0484189 -0.0979307 -0.1460206 -0.1926431 -0.2377554 -0.2813175 -0.3232916 -0.3636422 -0.4023354 -0.4393390 -0.4746221 -0.5081546 -0.5399072 -0.5698508 -0.5979629 -0.6242823 -0.6488806 -0.6718261 -0.6931839 -0.7130159 -0.7313808 -0.7483349 -0.7639317 -0.7782223 -0.7912557 -0.8030786 -0.8137360 -0.8232708 -0.8317245 -0.8391370 -0.8455466 -0.8509906 -0.8555050 -0.8591245 -0.8618831 -0.8638138 -0.8649487 -0.8653193 -0.8649566 -0.8638908 -0.8621516 -0.8597687 -0.8567709 -0.8531871 -0.8490459 -0.8443758 -0.8392050 -0.8335618 -0.8274747 -0.8209718 -0.8140815 -0.8068326 -0.7992536 -0.7913736 -0.7832216 -0.7748272 -0.7662199 -0.7574299 -0.7484875 -0.7394233 -0.7302685 -0.7210545
D130040H23Rik 2.1775048 2.1049651 2.0337824 1.9639387 1.8954158 1.8281954 1.7622593 1.6975892 1.6341669 1.5719740 1.5109923 1.4512036 1.3925896 1.3351323 1.2788136 1.2236154 1.1695199 1.1165093 1.0645659 1.0136720 0.9638104 0.9149635 0.8671142 0.8202455 0.7743355 0.7293391 0.6852062 0.6418896 0.5993445 0.5575284 0.5164015 0.4759259 0.4360661 0.3967887 0.3580622 0.3198571 0.2821459 0.2449026 0.2081034 0.1717258 0.1357493 0.1001548 0.0649247 0.0300432 -0.0045042 -0.0387307 -0.0726480 -0.1062663 -0.1395948 -0.1726411 -0.2054120 -0.2379126 -0.2701457 -0.3020965 -0.3337418 -0.3650597 -0.3960298 -0.4266331 -0.4568519 -0.4866702 -0.5160729 -0.5450465 -0.5735787 -0.6016586 -0.6292761 -0.6564227 -0.6830908 -0.7092739 -0.7349667 -0.7601645 -0.7848641 -0.8090627 -0.8327588 -0.8559514 -0.8786406 -0.9008268 -0.9225116 -0.9436968 -0.9643853 -0.9845801 -1.0042851 -1.0235046 -1.0422432 -1.0605062 -1.0782991 -1.0956278 -1.1124987 -1.1289182 -1.1448933 -1.1604309 -1.1755384 -1.1902232 -1.2044931 -1.2183556 -1.2318189 -1.2448908 -1.2575794 -1.2698928 -1.2818392 -1.2934267
D3Ertd254e 2.6057166 2.4949461 2.3858907 2.2786514 2.1733226 2.0699916 1.9687397 1.8696416 1.7727668 1.6781788 1.5859362 1.4960929 1.4086979 1.3237964 1.2414296 1.1616353 1.0844481 1.0099001 0.9380205 0.8688367 0.8023743 0.7386576 0.6777097 0.6195530 0.5641859 0.5114928 0.4613285 0.4135543 0.3680374 0.3246505 0.2832716 0.2437830 0.2060718 0.1700290 0.1355494 0.1025312 0.0708761 0.0404887 0.0112762 -0.0168514 -0.0439816 -0.0701999 -0.0955894 -0.1202316 -0.1442059 -0.1675900 -0.1904600 -0.2128905 -0.2349546 -0.2567240 -0.2782688 -0.2996582 -0.3209558 -0.3421842 -0.3633430 -0.3844315 -0.4054489 -0.4263945 -0.4472676 -0.4680676 -0.4887939 -0.5094457 -0.5300226 -0.5505237 -0.5709486 -0.5912968 -0.6115675 -0.6317603 -0.6518746 -0.6719099 -0.6918657 -0.7117415 -0.7315369 -0.7512513 -0.7708843 -0.7904354 -0.8099043 -0.8292905 -0.8485935 -0.8678132 -0.8869489 -0.9060005 -0.9249674 -0.9438495 -0.9626463 -0.9813576 -0.9999830 -1.0185223 -1.0369752 -1.0553413 -1.0736205 -1.0918125 -1.1099171 -1.1279340 -1.1458630 -1.1637040 -1.1814567 -1.1991210 -1.2166966 -1.2341835
Heyl 2.3614700 2.2781329 2.1963424 2.1160624 2.0372579 1.9598947 1.8839401 1.8093620 1.7361296 1.6642127 1.5935823 1.5242103 1.4560692 1.3891326 1.3233748 1.2587709 1.1952967 1.1329290 1.0716449 1.0114226 0.9522406 0.8940784 0.8369159 0.7807338 0.7255181 0.6712798 0.6180350 0.5657975 0.5145793 0.4643898 0.4152368 0.3671260 0.3200614 0.2740455 0.2290789 0.1851610 0.1422898 0.1004620 0.0596732 0.0199177 -0.0188108 -0.0565199 -0.0932178 -0.1289133 -0.1636161 -0.1973365 -0.2300850 -0.2618727 -0.2927113 -0.3226123 -0.3515880 -0.3796503 -0.4068133 -0.4331061 -0.4585654 -0.4832261 -0.5071219 -0.5302848 -0.5527454 -0.5745329 -0.5956753 -0.6161993 -0.6361307 -0.6554938 -0.6743122 -0.6926083 -0.7104038 -0.7277192 -0.7445745 -0.7609886 -0.7769797 -0.7925654 -0.8077625 -0.8225871 -0.8370547 -0.8511804 -0.8649783 -0.8784624 -0.8916458 -0.9045413 -0.9171613 -0.9295175 -0.9416214 -0.9534838 -0.9651154 -0.9765264 -0.9877265 -0.9987252 -1.0095316 -1.0201545 -1.0306023 -1.0408832 -1.0510051 -1.0609755 -1.0708017 -1.0804908 -1.0900495 -1.0994844 -1.1088018 -1.1180076
Zbtb5 2.8112578 2.5911097 2.3792975 2.1761099 1.9817612 1.7963991 1.6201122 1.4529374 1.2948676 1.1458587 1.0058365 0.8747036 0.7523455 0.6386369 0.5334471 0.4366456 0.3481073 0.2677172 0.1953756 0.1310023 0.0745414 0.0259664 -0.0147157 -0.0474586 -0.0722789 -0.0896641 -0.1001974 -0.1044064 -0.1027739 -0.0957473 -0.0837473 -0.0671754 -0.0464211 -0.0218678 0.0061014 0.0370986 0.0707265 0.1065748 0.1442163 0.1832044 0.2230706 0.2633231 0.3034458 0.3428982 0.3811162 0.4175136 0.4514847 0.4824076 0.5096491 0.5325697 0.5505306 0.5629009 0.5691073 0.5690140 0.5627527 0.5504880 0.5324125 0.5087440 0.4797229 0.4456096 0.4066817 0.3632310 0.3155612 0.2639848 0.2088208 0.1503920 0.0890227 0.0250362 -0.0412469 -0.1095114 -0.1794485 -0.2507579 -0.3231494 -0.3963437 -0.4700741 -0.5440868 -0.6181424 -0.6920157 -0.7654967 -0.8383907 -0.9105184 -0.9817160 -1.0518348 -1.1207414 -1.1883169 -1.2544568 -1.3190705 -1.3820803 -1.4434215 -1.5030410 -1.5608970 -1.6169584 -1.6712037 -1.7236205 -1.7742046 -1.8229596 -1.8698957 -1.9150295 -1.9583829 -1.9999827
Nkx6-2 2.7782970 2.5591456 2.3446750 2.1354347 1.9319273 1.7346102 1.5438975 1.3601628 1.1837418 1.0149359 0.8540150 0.7012214 0.5567736 0.4208704 0.2936945 0.1754172 0.0662028 -0.0337873 -0.1243897 -0.2054346 -0.2767404 -0.3381094 -0.3893221 -0.4301319 -0.4603999 -0.4806325 -0.4914969 -0.4936176 -0.4875838 -0.4739568 -0.4532761 -0.4260659 -0.3928400 -0.3541073 -0.3103759 -0.2621577 -0.2099717 -0.1543474 -0.0958276 -0.0349711 0.0276460 0.0914283 0.1557602 0.2200055 0.2835073 0.3455887 0.4055536 0.4626886 0.5162651 0.5655420 0.6097690 0.6481908 0.6801003 0.7052850 0.7238281 0.7358329 0.7414186 0.7407189 0.7338815 0.7210667 0.7024464 0.6782030 0.6485288 0.6136244 0.5736982 0.5289649 0.4796452 0.4259643 0.3681512 0.3064379 0.2410586 0.1722483 0.1002428 0.0252774 -0.0524136 -0.1325977 -0.2150450 -0.2995284 -0.3858246 -0.4737147 -0.5629841 -0.6534237 -0.7448299 -0.8370051 -0.9297581 -1.0229044 -1.1162662 -1.2096731 -1.3029617 -1.3959764 -1.4885690 -1.5805988 -1.6719329 -1.7624461 -1.8520207 -1.9405465 -2.0279209 -2.1140484 -2.1988409 -2.2822170
Rxrg 1.2923771 1.1786689 1.0674405 0.9590672 0.8538940 0.7522376 0.6543879 0.5606107 0.4711493 0.3862277 0.3060526 0.2308168 0.1607016 0.0958801 0.0365205 -0.0172108 -0.0651459 -0.1071116 -0.1429259 -0.1723941 -0.1953048 -0.2114254 -0.2204977 -0.2222332 -0.2164219 -0.2033769 -0.1835507 -0.1573721 -0.1252529 -0.0875954 -0.0447982 0.0027382 0.0546060 0.1103850 0.1696392 0.2319118 0.2967227 0.3635654 0.4319047 0.5011750 0.5707793 0.6400889 0.7084436 0.7751530 0.8394985 0.9007356 0.9580980 1.0108016 1.0580504 1.0990421 1.1329756 1.1590586 1.1765678 1.1853195 1.1854603 1.1771767 1.1606890 1.1362489 1.1041364 1.0646575 1.0181410 0.9649362 0.9054096 0.8399426 0.7689287 0.6927707 0.6118781 0.5266646 0.4375459 0.3449369 0.2492496 0.1508912 0.0502617 -0.0522477 -0.1562565 -0.2613965 -0.3673131 -0.4736668 -0.5801341 -0.6864087 -0.7922019 -0.8972435 -1.0012824 -1.1040864 -1.2054426 -1.3051576 -1.4030570 -1.4989852 -1.5928050 -1.6843972 -1.7736598 -1.8605075 -1.9448708 -2.0266950 -2.1059398 -2.1825779 -2.2565945 -2.3279858 -2.3967587 -2.4629293
Pax6 1.3795954 1.2756736 1.1740674 1.0751188 0.9791412 0.8864207 0.7972177 0.7117689 0.6302893 0.5529743 0.4800028 0.4115390 0.3477358 0.2887376 0.2346831 0.1857087 0.1419517 0.1035536 0.0706639 0.0434435 0.0220686 0.0067352 -0.0023373 -0.0049007 -0.0007783 0.0097297 0.0261963 0.0482168 0.0754016 0.1073690 0.1437399 0.1841315 0.2281529 0.2754002 0.3254526 0.3778690 0.4321851 0.4879109 0.5445291 0.6014942 0.6582321 0.7141401 0.7685888 0.8209232 0.8704659 0.9165207 0.9583767 0.9953135 1.0266075 1.0515386 1.0693977 1.0794952 1.0812177 1.0744626 1.0594395 1.0363998 1.0056296 0.9674473 0.9221999 0.8702601 0.8120229 0.7479025 0.6783290 0.6037449 0.5246025 0.4413601 0.3544794 0.2644222 0.1716473 0.0766080 -0.0202509 -0.1184956 -0.2177057 -0.3174766 -0.4174213 -0.5171723 -0.6163833 -0.7147306 -0.8119138 -0.9076570 -1.0017092 -1.0938446 -1.1838627 -1.2715879 -1.3568694 -1.4395804 -1.5196173 -1.5968984 -1.6713633 -1.7429714 -1.8117004 -1.8775451 -1.9405157 -2.0006367 -2.0579450 -2.1124886 -2.1643254 -2.2135214 -2.2601495 -2.3042887
Rit1 1.5555199 1.4676359 1.3808177 1.2953330 1.2114395 1.1293857 1.0494106 0.9717449 0.8966110 0.8242239 0.7547917 0.6885165 0.6255953 0.5662205 0.5105812 0.4588638 0.4112537 0.3679354 0.3290948 0.2949193 0.2656001 0.2413327 0.2223188 0.2087679 0.2008133 0.1981837 0.2004919 0.2073600 0.2184170 0.2332967 0.2516363 0.2730737 0.2972471 0.3237927 0.3523441 0.3825310 0.4139786 0.4463066 0.4791291 0.5120538 0.5446827 0.5766112 0.6074290 0.6367204 0.6640650 0.6890382 0.7112128 0.7301598 0.7454503 0.7566564 0.7633538 0.7651236 0.7615856 0.7526799 0.7385349 0.7192900 0.6950926 0.6660976 0.6324665 0.5943670 0.5519718 0.5054584 0.4550082 0.4008059 0.3430388 0.2818964 0.2175693 0.1502491 0.0801277 0.0073966 -0.0677535 -0.1451331 -0.2245546 -0.3058326 -0.3887843 -0.4732302 -0.5589939 -0.6459029 -0.7337890 -0.8224881 -0.9118408 -1.0016927 -1.0918944 -1.1823018 -1.2727762 -1.3631844 -1.4533990 -1.5432981 -1.6327658 -1.7216918 -1.8099718 -1.8975071 -1.9842050 -2.0699782 -2.1547452 -2.2384300 -2.3209621 -2.4022761 -2.4823119 -2.5610144
Tsc22d3 1.7908200 1.6989762 1.6081299 1.5185296 1.4304158 1.3440207 1.2595689 1.1772774 1.0973562 1.0200087 0.9454321 0.8738181 0.8053535 0.7402205 0.6785978 0.6206613 0.5665847 0.5165403 0.4707002 0.4292369 0.3923245 0.3601395 0.3328622 0.3106774 0.2936993 0.2816742 0.2742435 0.2710569 0.2717709 0.2760471 0.2835512 0.2939512 0.3069168 0.3221178 0.3392238 0.3579031 0.3778221 0.3986449 0.4200327 0.4416439 0.4631334 0.4841533 0.5043524 0.5233767 0.5408700 0.5564739 0.5698288 0.5805748 0.5883522 0.5928027 0.5935707 0.5903045 0.5826841 0.5706606 0.5543423 0.5338450 0.5092892 0.4807997 0.4485053 0.4125386 0.3730350 0.3301328 0.2839727 0.2346972 0.1824504 0.1273776 0.0696250 0.0093391 -0.0533333 -0.1182457 -0.1852519 -0.2542067 -0.3249659 -0.3973868 -0.4713282 -0.5466508 -0.6232175 -0.7008935 -0.7795464 -0.8590469 -0.9392682 -1.0200870 -1.1013829 -1.1830391 -1.2649421 -1.3469821 -1.4290530 -1.5110525 -1.5928819 -1.6744466 -1.7556559 -1.8364228 -1.9166645 -1.9963020 -2.0752601 -2.1534677 -2.2308575 -2.3073657 -2.3829326 -2.4575021
Arntl 1.7438245 1.6424515 1.5430140 1.4457834 1.3510119 1.2589339 1.1697666 1.0837115 1.0009560 0.9216740 0.8460282 0.7741711 0.7062469 0.6423929 0.5827413 0.5274210 0.4765593 0.4302838 0.3887243 0.3520148 0.3202955 0.2937149 0.2724324 0.2566201 0.2463807 0.2414194 0.2413341 0.2457394 0.2542624 0.2665393 0.2822120 0.3009252 0.3223238 0.3460508 0.3717447 0.3990385 0.4275575 0.4569189 0.4867304 0.5165900 0.5460855 0.5747953 0.6022880 0.6281241 0.6518570 0.6730342 0.6912001 0.7058978 0.7166722 0.7230730 0.7246584 0.7209990 0.7117141 0.6967676 0.6763274 0.6505799 0.6197263 0.5839805 0.5435681 0.4987245 0.4496934 0.3967249 0.3400747 0.2800019 0.2167681 0.1506357 0.0818667 0.0107216 -0.0625421 -0.1376707 -0.2144153 -0.2925330 -0.3717875 -0.4519499 -0.5327994 -0.6141241 -0.6957209 -0.7773967 -0.8589681 -0.9402620 -1.0211157 -1.1013770 -1.1809043 -1.2595662 -1.3372422 -1.4138219 -1.4892049 -1.5633009 -1.6360290 -1.7073178 -1.7771046 -1.8453356 -1.9119650 -1.9769549 -2.0402747 -2.1019007 -2.1618160 -2.2200094 -2.2764757 -2.3312146
Nfib 0.1628424 0.1667088 0.1706506 0.1747423 0.1790588 0.1836747 0.1886648 0.1941043 0.2000680 0.2066312 0.2138693 0.2218578 0.2306724 0.2403891 0.2510843 0.2628344 0.2757163 0.2898074 0.3051855 0.3219287 0.3401158 0.3598261 0.3811396 0.4041370 0.4288599 0.4551560 0.4828126 0.5116163 0.5413525 0.5718054 0.6027580 0.6339919 0.6652875 0.6964236 0.7271778 0.7573265 0.7866446 0.8149061 0.8418839 0.8673499 0.8910754 0.9128309 0.9323868 0.9495131 0.9639801 0.9755584 0.9840191 0.9891344 0.9906778 0.9884244 0.9821513 0.9716380 0.9566861 0.9372898 0.9135545 0.8855896 0.8535064 0.8174183 0.7774405 0.7336900 0.6862852 0.6353459 0.5809931 0.5233490 0.4625367 0.3986801 0.3319039 0.2623331 0.1900933 0.1153104 0.0381103 -0.0413808 -0.1230372 -0.2067330 -0.2923430 -0.3797424 -0.4688068 -0.5594127 -0.6514376 -0.7447598 -0.8392586 -0.9348146 -1.0313100 -1.1286280 -1.2266538 -1.3252738 -1.4243765 -1.5238523 -1.6235935 -1.7234943 -1.8234513 -1.9233632 -2.0231313 -2.1226590 -2.2218523 -2.3206197 -2.4188724 -2.5165242 -2.6134916 -2.7096938
Nfe2l2 1.0277721 0.9660517 0.9053617 0.8459415 0.7880180 0.7318061 0.6775098 0.6253228 0.5754295 0.5280061 0.4832216 0.4412391 0.4022174 0.3663117 0.3336757 0.3044628 0.2788278 0.2569288 0.2389285 0.2249967 0.2153121 0.2100643 0.2094562 0.2137067 0.2229690 0.2370026 0.2554544 0.2779792 0.3042359 0.3338839 0.3665794 0.4019727 0.4397053 0.4794079 0.5206978 0.5631778 0.6064348 0.6500388 0.6935424 0.7364812 0.7783738 0.8187231 0.8570173 0.8927323 0.9253340 0.9542814 0.9790299 0.9990356 1.0137602 1.0226756 1.0252697 1.0210525 1.0096003 0.9908999 0.9651855 0.9327213 0.8937963 0.8487216 0.7978274 0.7414602 0.6799801 0.6137582 0.5431733 0.4686097 0.3904548 0.3090960 0.2249188 0.1383045 0.0496279 -0.0407446 -0.1324566 -0.2251635 -0.3185343 -0.4122522 -0.5060164 -0.5995425 -0.6925637 -0.7848311 -0.8761143 -0.9662014 -1.0548993 -1.1420335 -1.2274480 -1.3110050 -1.3925841 -1.4720821 -1.5494124 -1.6245038 -1.6973001 -1.7677594 -1.8358524 -1.9015626 -1.9648845 -2.0258230 -2.0843924 -2.1406157 -2.1945233 -2.2461523 -2.2955459 -2.3427523
Meis2 0.7917188 0.7563692 0.7214179 0.6870354 0.6533879 0.6206373 0.5889418 0.5584557 0.5293300 0.5017128 0.4757496 0.4515838 0.4293572 0.4092107 0.3912848 0.3757204 0.3626595 0.3522456 0.3446253 0.3399485 0.3383696 0.3400485 0.3451517 0.3538533 0.3662692 0.3821953 0.4013312 0.4233778 0.4480355 0.4750024 0.5039726 0.5346349 0.5666717 0.5997579 0.6335606 0.6677381 0.7019401 0.7358071 0.7689714 0.8010566 0.8316791 0.8604485 0.8869690 0.9108404 0.9316604 0.9490258 0.9625351 0.9717903 0.9764002 0.9759826 0.9701676 0.9586008 0.9409767 0.9173076 0.8877943 0.8526555 0.8121240 0.7664455 0.7158772 0.6606863 0.6011484 0.5375466 0.4701697 0.3993108 0.3252662 0.2483339 0.1688123 0.0869986 0.0031882 -0.0823273 -0.1692610 -0.2573315 -0.3462648 -0.4357947 -0.5256639 -0.6156250 -0.7054416 -0.7948884 -0.8837524 -0.9718330 -1.0589431 -1.1449086 -1.2295693 -1.3127789 -1.3944047 -1.4743280 -1.5524437 -1.6286602 -1.7028988 -1.7750938 -1.8451912 -1.9131494 -1.9789373 -2.0425346 -2.1039309 -2.1631248 -2.2201235 -2.2749418 -2.3276017 -2.3781316
Id2 0.8958120 0.8541181 0.8127755 0.7719685 0.7318786 0.6926838 0.6545595 0.6176778 0.5822082 0.5483175 0.5161700 0.4859279 0.4577516 0.4318000 0.4082311 0.3872023 0.3688711 0.3533958 0.3409358 0.3316526 0.3257104 0.3232770 0.3245244 0.3296297 0.3387070 0.3515389 0.3678079 0.3871987 0.4093962 0.4340844 0.4609454 0.4896584 0.5198988 0.5513381 0.5836430 0.6164755 0.6494923 0.6823455 0.7146823 0.7461454 0.7763734 0.8050014 0.8316614 0.8559831 0.8775949 0.8961243 0.9111993 0.9224491 0.9295055 0.9320042 0.9295858 0.9218979 0.9086246 0.8897426 0.8653995 0.8357529 0.8009683 0.7612187 0.7166842 0.6675523 0.6140174 0.5562808 0.4945507 0.4290416 0.3599749 0.2875782 0.2120852 0.1337356 0.0527748 -0.0305466 -0.1159729 -0.2032445 -0.2920977 -0.3822659 -0.4734806 -0.5654717 -0.6579694 -0.7507047 -0.8434112 -0.9358262 -1.0276924 -1.1187592 -1.2087847 -1.2975368 -1.3847954 -1.4703533 -1.5540181 -1.6356134 -1.7149797 -1.7919759 -1.8664795 -1.9383871 -2.0076153 -2.0740996 -2.1377952 -2.1986756 -2.2567322 -2.3119733 -2.3644227 -2.4141189 
write.table(heatmap_matrix_q_value_5_10_minus_5, file = file.path(tables_directory, "2-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6-significant_transcription_factors_diff_test_analysis_qval_5_10_minus_5_heatmap_matrix.txt"), sep="\t", quote=FALSE, row.names=FALSE)
2.2.2.1.2 q value < 0.01
significant_genes_q_value_0.01 <- filter(diff_test_res_all_genes, qval < 0.01) %>% .$gene 
cat("Number of significant genes: ", length(significant_genes_q_value_0.01))
## Number of significant genes:  7357
significant_transcription_factors_q_value_0.01 <- as.character(significant_genes_q_value_0.01[significant_genes_q_value_0.01 %in% transcription_factors$Symbol])
cat("Number of significant transcription factors:", length(significant_transcription_factors_q_value_0.01))
## Number of significant transcription factors: 384
plot_genes_heatmap_output_q_value_0.01 <- plot_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_0.01,], cluster_rows=TRUE, num_clusters=1, return_heatmap=TRUE, show_rownames = TRUE)

## <simpleError in checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon): NAs found in the working weights variable 'wz'>
save_pheatmap_pdf(plot_genes_heatmap_output_q_value_0.01[[2]], file.path("figures", "2-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6", "diff_test_plots_transcription_factors_only_q_value_0.01_heatmap_custom.pdf"), width=16, height=40)
## pdf 
##   2
heatmap_matrix_q_value_0.01 <- plot_genes_heatmap_output_q_value_0.01[[1]]
ph_res_q_value_0.01 <- plot_genes_heatmap_output_q_value_0.01[[2]]
pheatmap_ordering_q_value_0.01 <- rownames(heatmap_matrix_q_value_0.01[ph_res_q_value_0.01$tree_row[["order"]],])

transcription_factors_table_q_value_0.01 <- filter(diff_test_res_all_genes, gene %in% significant_transcription_factors_q_value_0.01)
# Put genes from the transcription factor table in the same order
transcription_factors_table_q_value_0.01 <- transcription_factors_table_q_value_0.01 %>% arrange(match(gene, pheatmap_ordering_q_value_0.01))

write.table(transcription_factors_table_q_value_0.01, file.path(tables_directory, "2-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6-significant_transcription_factors_diff_test_analysis_qval_0.01.txt"), sep="\t", quote=FALSE, row.names=FALSE)

heatmap_matrix_q_value_0.01 <- plot_genes_heatmap_output_q_value_0.01[[1]]
heatmap_matrix_q_value_0.01 <- as.data.frame(heatmap_matrix_q_value_0.01) %>% rownames_to_column("gene")
heatmap_matrix_q_value_0.01 <- heatmap_matrix_q_value_0.01 %>% arrange(match(gene, pheatmap_ordering_q_value_0.01))
heatmap_matrix_q_value_0.01 %>% head(20) %>% kable() %>% kable_styling() %>% scroll_box(height="200px", width="600px")
gene 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100
Pou3f2 -0.1297400 -0.0154223 0.0996139 0.2148745 0.3298456 0.4439934 0.5567651 0.6675897 0.7758786 0.8810272 0.9824160 1.0794130 1.1713751 1.2576504 1.3375813 1.4105066 1.4757646 1.5326969 1.5806511 1.6189851 1.6470708 1.6642984 1.6700805 1.6638570 1.6452683 1.6148154 1.5732786 1.5214585 1.4601698 1.3902364 1.3124859 1.2277455 1.1368372 1.0405744 0.9397585 0.8351754 0.7275936 0.6177615 0.5064061 0.3942310 0.2819159 0.1701162 0.0594620 -0.0494410 -0.1560111 -0.2596901 -0.3599419 -0.4562510 -0.5481207 -0.6350710 -0.7166363 -0.7923628 -0.8618465 -0.9250958 -0.9823434 -1.0338113 -1.0797086 -1.1202328 -1.1555702 -1.1858968 -1.2113791 -1.2321747 -1.2484330 -1.2602957 -1.2678978 -1.2713675 -1.2708276 -1.2663953 -1.2581831 -1.2462990 -1.2308473 -1.2119290 -1.1896419 -1.1640812 -1.1353400 -1.1035098 -1.0686804 -1.0309405 -0.9903784 -0.9470817 -0.9011380 -0.8526352 -0.8016617 -0.7483065 -0.6926599 -0.6348136 -0.5748606 -0.5128960 -0.4490167 -0.3833220 -0.3159136 -0.2468960 -0.1763762 -0.1044645 -0.0312741 0.0430783 0.1184729 0.1947863 0.2718913 0.3496575
Sp6 0.5839400 0.5938060 0.6039331 0.6145201 0.6257716 0.6378991 0.6511220 0.6656688 0.6817789 0.6997049 0.7197148 0.7420951 0.7671546 0.7952279 0.8266807 0.8619151 0.9013762 0.9455596 0.9950205 1.0503840 1.1123574 1.1817451 1.2594654 1.3465714 1.4435754 1.5474623 1.6534536 1.7558789 1.8481991 1.9231748 1.9732066 1.9908545 1.9695176 1.9042177 1.7923907 1.6345551 1.4347129 1.2003503 0.9419577 0.6720730 0.4039581 0.1501115 -0.0791159 -0.2765450 -0.4386476 -0.5654235 -0.6597598 -0.7264654 -0.7712238 -0.7996785 -0.8167904 -0.8265083 -0.8317101 -0.8343260 -0.8355620 -0.8361119 -0.8363426 -0.8364341 -0.8364685 -0.8364807 -0.8364849 -0.8364862 -0.8364866 -0.8364867 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868 -0.8364868
Irx3 2.0868433 2.0293431 1.9719996 1.9147184 1.8574065 1.7999728 1.7423279 1.6843840 1.6260552 1.5672573 1.5079080 1.4479267 1.3872349 1.3257560 1.2634155 1.2001409 1.1358619 1.0705106 1.0040213 0.9363307 0.8673781 0.7971054 0.7254570 0.6523805 0.5778709 0.5021436 0.4254760 0.3481387 0.2703957 0.1925038 0.1147131 0.0372661 -0.0396016 -0.1156614 -0.1906918 -0.2644782 -0.3368125 -0.4074930 -0.4763238 -0.5431149 -0.6076815 -0.6698437 -0.7294258 -0.7862560 -0.8401657 -0.8909890 -0.9385620 -0.9827221 -1.0233073 -1.0601556 -1.0931039 -1.1219875 -1.1466565 -1.1671324 -1.1835312 -1.1959634 -1.2045335 -1.2093403 -1.2104776 -1.2080341 -1.2020942 -1.1927381 -1.1800423 -1.1640799 -1.1449206 -1.1226317 -1.0972777 -1.0689209 -1.0376217 -1.0034387 -0.9664293 -0.9266495 -0.8841544 -0.8389985 -0.7912356 -0.7409196 -0.6881040 -0.6328429 -0.5751904 -0.5152015 -0.4529319 -0.3884382 -0.3217784 -0.2530117 -0.1821989 -0.1094025 -0.0346870 0.0418813 0.1202337 0.2002991 0.2820041 0.3652726 0.4500256 0.5361814 0.6236553 0.7123595 0.8022030 0.8930914 0.9849271 1.0776091
Rora 2.2655226 2.1976372 2.1300251 2.0626244 1.9953746 1.9282164 1.8610915 1.7939432 1.7267158 1.6593550 1.5918075 1.5240216 1.4559467 1.3875337 1.3187346 1.2495029 1.1797935 1.1095627 1.0387683 0.9673693 0.8953266 0.8226024 0.7491605 0.6749663 0.6000216 0.5244968 0.4486094 0.3725718 0.2965908 0.2208676 0.1455983 0.0709731 -0.0028230 -0.0756103 -0.1472145 -0.2174661 -0.2862006 -0.3532582 -0.4184832 -0.4817242 -0.5428335 -0.6016669 -0.6580833 -0.7119441 -0.7631132 -0.8114562 -0.8568401 -0.8991328 -0.9382024 -0.9739171 -1.0061441 -1.0347492 -1.0596114 -1.0807534 -1.0982781 -1.1122840 -1.1228651 -1.1301108 -1.1341066 -1.1349342 -1.1326717 -1.1273941 -1.1191733 -1.1080786 -1.0941767 -1.0775324 -1.0582082 -1.0362650 -1.0117619 -0.9847570 -0.9553071 -0.9234679 -0.8892945 -0.8528415 -0.8141629 -0.7733126 -0.7303444 -0.6853122 -0.6382702 -0.5892729 -0.5383755 -0.4856339 -0.4311047 -0.3748457 -0.3169156 -0.2573744 -0.1962836 -0.1337059 -0.0697059 -0.0043496 0.0622950 0.1301582 0.1991683 0.2692515 0.3403318 0.4123311 0.4851692 0.5587634 0.6330286 0.7078775
Zfp112 0.8745833 0.9250182 0.9757078 1.0263301 1.0765490 1.1260144 1.1743630 1.2212187 1.2661940 1.3088907 1.3489019 1.3858140 1.4192085 1.4486648 1.4737632 1.4940875 1.5092291 1.5187901 1.5223876 1.5196576 1.5102593 1.4938796 1.4702374 1.4390878 1.4003333 1.3544330 1.3020230 1.2437480 1.1802542 1.1121830 1.0401661 0.9648198 0.8867414 0.8065054 0.7246610 0.6417294 0.5582025 0.4745417 0.3911775 0.3085092 0.2269054 0.1467048 0.0682171 -0.0082758 -0.0825179 -0.1542774 -0.2233452 -0.2895322 -0.3526675 -0.4125960 -0.4691763 -0.5222778 -0.5717985 -0.6178313 -0.6605687 -0.7001902 -0.7368623 -0.7707398 -0.8019663 -0.8306755 -0.8569918 -0.8810314 -0.9029026 -0.9227067 -0.9405385 -0.9564868 -0.9706352 -0.9830622 -0.9938416 -1.0030436 -1.0107341 -1.0169761 -1.0218292 -1.0253505 -1.0275945 -1.0286135 -1.0284581 -1.0271769 -1.0248172 -1.0214250 -1.0170453 -1.0117222 -1.0054990 -0.9984188 -0.9905240 -0.9818570 -0.9724600 -0.9623755 -0.9516460 -0.9403144 -0.9284241 -0.9160191 -0.9031437 -0.8898435 -0.8761643 -0.8621534 -0.8478586 -0.8333290 -0.8186146 -0.8037666
Atf7 1.2090613 1.2293352 1.2494540 1.2692130 1.2884055 1.3068230 1.3242556 1.3404920 1.3553198 1.3685259 1.3798967 1.3892185 1.3962784 1.4008643 1.4027656 1.4017738 1.3976836 1.3902927 1.3794035 1.3648232 1.3463650 1.3238488 1.2971022 1.2659612 1.2303341 1.1904441 1.1466110 1.0991549 1.0483952 0.9946492 0.9382312 0.8794516 0.8186155 0.7560227 0.6919664 0.6267329 0.5606011 0.4938422 0.4267193 0.3594870 0.2923919 0.2256720 0.1595568 0.0942679 0.0300185 -0.0329858 -0.0945468 -0.1544736 -0.2125816 -0.2686928 -0.3226344 -0.3742390 -0.4233584 -0.4699989 -0.5142512 -0.5562032 -0.5959394 -0.6335412 -0.6690867 -0.7026510 -0.7343066 -0.7641234 -0.7921689 -0.8185084 -0.8432048 -0.8663194 -0.8879114 -0.9080383 -0.9267560 -0.9441189 -0.9601802 -0.9749913 -0.9886031 -1.0010647 -1.0124247 -1.0227305 -1.0320288 -1.0403653 -1.0477853 -1.0543332 -1.0600528 -1.0649878 -1.0691808 -1.0726746 -1.0755112 -1.0777326 -1.0793803 -1.0804958 -1.0811202 -1.0812946 -1.0810600 -1.0804572 -1.0795270 -1.0783103 -1.0768476 -1.0751799 -1.0733478 -1.0713923 -1.0693542 -1.0672743
Zfp521 1.3555900 1.3713142 1.3868412 1.4019436 1.4163922 1.4299564 1.4424048 1.4535045 1.4630225 1.4707253 1.4763798 1.4797536 1.4806155 1.4787364 1.4738899 1.4658529 1.4544064 1.4393365 1.4204353 1.3975018 1.3703428 1.3387739 1.3026209 1.2617203 1.2159935 1.1657267 1.1113163 1.0531569 0.9916403 0.9271533 0.8600767 0.7907841 0.7196406 0.6470022 0.5732148 0.4986137 0.4235233 0.3482564 0.2731145 0.1983871 0.1243525 0.0512774 -0.0205828 -0.0909831 -0.1596892 -0.2264764 -0.2911292 -0.3534404 -0.4132106 -0.4702471 -0.5243634 -0.5753776 -0.6231301 -0.6676447 -0.7090449 -0.7474490 -0.7829697 -0.8157141 -0.8457845 -0.8732780 -0.8982878 -0.9209027 -0.9412077 -0.9592845 -0.9752111 -0.9890630 -1.0009125 -1.0108296 -1.0188818 -1.0251345 -1.0296512 -1.0324934 -1.0337214 -1.0333936 -1.0315676 -1.0282995 -1.0236447 -1.0176575 -1.0103917 -1.0019004 -0.9922364 -0.9814520 -0.9695992 -0.9567301 -0.9428966 -0.9281507 -0.9125446 -0.8961306 -0.8789614 -0.8610901 -0.8425703 -0.8234560 -0.8038017 -0.7836628 -0.7630951 -0.7421554 -0.7209009 -0.6993899 -0.6776814 -0.6558352
Zfp768 1.7015702 1.6867105 1.6717388 1.6565224 1.6409293 1.6248286 1.6080900 1.5905845 1.5721838 1.5527612 1.5321908 1.5103486 1.4871119 1.4623599 1.4359737 1.4078365 1.3778339 1.3458540 1.3117879 1.2755296 1.2369764 1.1960293 1.1525933 1.1065771 1.0579378 1.0068476 0.9535423 0.8982551 0.8412159 0.7826511 0.7227832 0.6618302 0.6000059 0.5375188 0.4745729 0.4113667 0.3480938 0.2849424 0.2220953 0.1597304 0.0980200 0.0371318 -0.0227719 -0.0815331 -0.1389987 -0.1950197 -0.2494513 -0.3021523 -0.3529851 -0.4018151 -0.4485105 -0.4929418 -0.5349940 -0.5746766 -0.6120682 -0.6472452 -0.6802815 -0.7112481 -0.7402140 -0.7672455 -0.7924071 -0.8157611 -0.8373679 -0.8572863 -0.8755734 -0.8922848 -0.9074745 -0.9211956 -0.9334994 -0.9444366 -0.9540566 -0.9624078 -0.9695378 -0.9754936 -0.9803210 -0.9840657 -0.9867724 -0.9884854 -0.9892487 -0.9891056 -0.9880993 -0.9862725 -0.9836680 -0.9803279 -0.9762947 -0.9716103 -0.9663167 -0.9604561 -0.9540704 -0.9472016 -0.9398919 -0.9321834 -0.9241184 -0.9157394 -0.9070889 -0.8982097 -0.8891448 -0.8799372 -0.8706305 -0.8612680
Epas1 1.5483476 1.5479212 1.5472907 1.5462522 1.5446019 1.5421370 1.5386553 1.5339564 1.5278421 1.5201168 1.5105889 1.4990712 1.4853825 1.4693482 1.4508017 1.4295857 1.4055536 1.3785707 1.3485158 1.3152823 1.2787803 1.2389371 1.1956993 1.1490337 1.0989829 1.0458695 0.9900946 0.9320508 0.8721196 0.8106691 0.7480520 0.6846040 0.6206421 0.5564639 0.4923469 0.4285480 0.3653033 0.3028282 0.2413179 0.1809474 0.1218727 0.0642314 0.0081434 -0.0462876 -0.0989737 -0.1498408 -0.1988283 -0.2458874 -0.2909797 -0.3340765 -0.3751576 -0.4142094 -0.4512326 -0.4863069 -0.5195503 -0.5510732 -0.5809785 -0.6093625 -0.6363150 -0.6619199 -0.6862557 -0.7093960 -0.7314096 -0.7523612 -0.7723114 -0.7913171 -0.8094318 -0.8267059 -0.8431868 -0.8589193 -0.8739455 -0.8883053 -0.9020363 -0.9151743 -0.9277531 -0.9398047 -0.9513595 -0.9624464 -0.9730931 -0.9833258 -0.9931694 -1.0026479 -1.0117841 -1.0205999 -1.0291163 -1.0373533 -1.0453303 -1.0530657 -1.0605774 -1.0678826 -1.0749979 -1.0819392 -1.0887219 -1.0953610 -1.1018707 -1.1082651 -1.1145575 -1.1207610 -1.1268882 -1.1329512
Nr3c2 1.3601806 1.3894666 1.4186106 1.4472205 1.4748919 1.5012095 1.5257484 1.5480754 1.5677513 1.5843341 1.5973815 1.6064551 1.6111242 1.6109706 1.6055932 1.5946137 1.5776815 1.5544802 1.5247325 1.4882066 1.4447215 1.3941521 1.3364343 1.2715693 1.1997494 1.1218119 1.0387691 0.9516035 0.8612568 0.7686201 0.6745267 0.5797467 0.4849838 0.3908731 0.2979813 0.2068076 0.1177857 0.0312873 -0.0523748 -0.1329418 -0.2102047 -0.2839990 -0.3542001 -0.4207180 -0.4834924 -0.5424883 -0.5976907 -0.6491009 -0.6967317 -0.7406038 -0.7807420 -0.8171712 -0.8499298 -0.8792065 -0.9052557 -0.9283040 -0.9485526 -0.9661799 -0.9813441 -0.9941850 -1.0048266 -1.0133779 -1.0199353 -1.0245829 -1.0273944 -1.0284341 -1.0277572 -1.0254112 -1.0214366 -1.0158672 -1.0087311 -1.0000509 -0.9898446 -0.9781257 -0.9649038 -0.9501853 -0.9339731 -0.9162676 -0.8970671 -0.8763675 -0.8541634 -0.8304482 -0.8052142 -0.7784534 -0.7501577 -0.7203190 -0.6889303 -0.6559853 -0.6214796 -0.5854105 -0.5477779 -0.5085844 -0.4678364 -0.4255439 -0.3817216 -0.3363889 -0.2895711 -0.2412994 -0.1916118 -0.1405536
Gli2 2.1082610 2.0598239 2.0116998 1.9637939 1.9160147 1.8682738 1.8204861 1.7725695 1.7244449 1.6760368 1.6272724 1.5780827 1.5284016 1.4781667 1.4273186 1.3758021 1.3235650 1.2705591 1.2167399 1.1620670 1.1065037 1.0500174 0.9925798 0.9341668 0.8747891 0.8146074 0.7538216 0.6926234 0.6311961 0.5697145 0.5083448 0.4472447 0.3865632 0.3264409 0.2670100 0.2083948 0.1507114 0.0940686 0.0385679 -0.0156962 -0.0686357 -0.1201688 -0.1702192 -0.2187163 -0.2655940 -0.3107908 -0.3542491 -0.3959147 -0.4357365 -0.4736660 -0.5096563 -0.5436624 -0.5756484 -0.6056587 -0.6337802 -0.6600952 -0.6846817 -0.7076133 -0.7289597 -0.7487871 -0.7671580 -0.7841320 -0.7997657 -0.8141130 -0.8272253 -0.8391518 -0.8499393 -0.8596330 -0.8682760 -0.8759099 -0.8825746 -0.8883089 -0.8931501 -0.8971345 -0.9002972 -0.9026725 -0.9042938 -0.9051939 -0.9054048 -0.9049580 -0.9038845 -0.9022148 -0.8999793 -0.8972079 -0.8939305 -0.8901765 -0.8859757 -0.8813575 -0.8763513 -0.8709869 -0.8652939 -0.8593020 -0.8530414 -0.8465422 -0.8398348 -0.8329500 -0.8259187 -0.8187723 -0.8115423 -0.8042608
Dbp 2.2506833 2.1891815 2.1281030 2.0673983 2.0070196 1.9469207 1.8870565 1.8273835 1.7678598 1.7084447 1.6490989 1.5897846 1.5304656 1.4711068 1.4116749 1.3521377 1.2924647 1.2326267 1.1725962 1.1123470 1.0518544 0.9910954 0.9300483 0.8686932 0.8070328 0.7451737 0.6832502 0.6213917 0.5597230 0.4983641 0.4374302 0.3770316 0.3172743 0.2582593 0.2000835 0.1428392 0.0866146 0.0314940 -0.0224424 -0.0751179 -0.1264593 -0.1763968 -0.2248633 -0.2717947 -0.3171295 -0.3608083 -0.4027738 -0.4429703 -0.4813437 -0.5178410 -0.5524101 -0.5849992 -0.6155648 -0.6441384 -0.6707923 -0.6955962 -0.7186165 -0.7399168 -0.7595578 -0.7775980 -0.7940931 -0.8090970 -0.8226612 -0.8348355 -0.8456677 -0.8552042 -0.8634898 -0.8705677 -0.8764801 -0.8812678 -0.8849706 -0.8876273 -0.8892760 -0.8899536 -0.8896966 -0.8885408 -0.8865214 -0.8836732 -0.8800305 -0.8756274 -0.8704975 -0.8646744 -0.8581915 -0.8510820 -0.8433792 -0.8351162 -0.8263265 -0.8170433 -0.8073002 -0.7971309 -0.7865694 -0.7756497 -0.7644063 -0.7528740 -0.7410879 -0.7290834 -0.7168963 -0.7045628 -0.6921196 -0.6796035
Nr1d1 2.3092053 2.2408024 2.1731343 2.1061427 2.0397718 1.9739678 1.9086797 1.8438586 1.7794577 1.7154328 1.6517416 1.5883440 1.5252022 1.4622803 1.3995448 1.3369640 1.2745085 1.2121508 1.1498655 1.0876292 1.0254207 0.9632207 0.9010118 0.8387788 0.7765290 0.7143707 0.6524368 0.5908536 0.5297403 0.4692096 0.4093671 0.3503124 0.2921385 0.2349323 0.1787748 0.1237415 0.0699023 0.0173224 -0.0339383 -0.0838239 -0.1322831 -0.1792682 -0.2247351 -0.2686429 -0.3109537 -0.3516319 -0.3906443 -0.4279594 -0.4635472 -0.4973791 -0.5294269 -0.5596634 -0.5880675 -0.6146823 -0.6395842 -0.6628461 -0.6845366 -0.7047210 -0.7234609 -0.7408148 -0.7568385 -0.7715848 -0.7851040 -0.7974441 -0.8086510 -0.8187686 -0.8278388 -0.8359019 -0.8429966 -0.8491602 -0.8544286 -0.8588367 -0.8624181 -0.8652054 -0.8672306 -0.8685245 -0.8691175 -0.8690393 -0.8683189 -0.8669851 -0.8650661 -0.8625898 -0.8595839 -0.8560759 -0.8520931 -0.8476627 -0.8428120 -0.8375679 -0.8319580 -0.8260094 -0.8197496 -0.8132062 -0.8064072 -0.7993805 -0.7921546 -0.7847579 -0.7772194 -0.7695683 -0.7618342 -0.7540471
Klf9 2.3396649 2.2689335 2.1988336 2.1293311 2.0603931 1.9919880 1.9240851 1.8566550 1.7896695 1.7231015 1.6569250 1.5911152 1.5256486 1.4605025 1.3956556 1.3310877 1.2667796 1.2027135 1.1388725 1.0752409 1.0118042 0.9485490 0.8854630 0.8225352 0.7597726 0.6972650 0.6351234 0.5734536 0.5123565 0.4519277 0.3922583 0.3334340 0.2755362 0.2186412 0.1628212 0.1081437 0.0546721 0.0024661 -0.0484189 -0.0979307 -0.1460206 -0.1926431 -0.2377554 -0.2813175 -0.3232916 -0.3636422 -0.4023354 -0.4393390 -0.4746221 -0.5081546 -0.5399072 -0.5698508 -0.5979629 -0.6242823 -0.6488806 -0.6718261 -0.6931839 -0.7130159 -0.7313808 -0.7483349 -0.7639317 -0.7782223 -0.7912557 -0.8030786 -0.8137360 -0.8232708 -0.8317245 -0.8391370 -0.8455466 -0.8509906 -0.8555050 -0.8591245 -0.8618831 -0.8638138 -0.8649487 -0.8653193 -0.8649566 -0.8638908 -0.8621516 -0.8597687 -0.8567709 -0.8531871 -0.8490459 -0.8443758 -0.8392050 -0.8335618 -0.8274747 -0.8209718 -0.8140815 -0.8068326 -0.7992536 -0.7913736 -0.7832216 -0.7748272 -0.7662199 -0.7574299 -0.7484875 -0.7394233 -0.7302685 -0.7210545
Hif3a 3.0000000 3.0000000 2.9336435 2.6986453 2.4776628 2.2702153 2.0757922 1.8938623 1.7238819 1.5653023 1.4175756 1.2801608 1.1525278 1.0341617 0.9245657 0.8232639 0.7298032 0.6437549 0.5647163 0.4923111 0.4261906 0.3660339 0.3115483 0.2624699 0.2185153 0.1792038 0.1440418 0.1125895 0.0844536 0.0592799 0.0367478 0.0165649 -0.0015370 -0.0178060 -0.0324726 -0.0457533 -0.0578520 -0.0689625 -0.0792700 -0.0889519 -0.0981797 -0.1071188 -0.1159298 -0.1247683 -0.1337850 -0.1431259 -0.1529316 -0.1633370 -0.1744705 -0.1864533 -0.1993982 -0.2134088 -0.2285682 -0.2448497 -0.2621653 -0.2804255 -0.2995401 -0.3194188 -0.3399725 -0.3611127 -0.3827530 -0.4048088 -0.4271983 -0.4498425 -0.4726653 -0.4955945 -0.5185611 -0.5415003 -0.5643511 -0.5870564 -0.6095635 -0.6318236 -0.6537921 -0.6754284 -0.6966960 -0.7175624 -0.7379985 -0.7579794 -0.7774834 -0.7964921 -0.8149906 -0.8329668 -0.8504115 -0.8673183 -0.8836829 -0.8995038 -0.9147811 -0.9295173 -0.9437163 -0.9573838 -0.9705267 -0.9831534 -0.9952731 -1.0068963 -1.0180341 -1.0286983 -1.0389015 -1.0486564 -1.0579765 -1.0668751
Zscan2 3.0000000 3.0000000 3.0000000 2.8234181 2.6129709 2.4114810 2.2188710 2.0350363 1.8598491 1.6931620 1.5348124 1.3846251 1.2424161 1.1079953 0.9811692 0.8617433 0.7495248 0.6443243 0.5459577 0.4542485 0.3690287 0.2901413 0.2174407 0.1507952 0.0900368 0.0347738 -0.0154221 -0.0609420 -0.1021442 -0.1393576 -0.1728857 -0.2030092 -0.2299894 -0.2540697 -0.2754788 -0.2944317 -0.3111324 -0.3257748 -0.3385442 -0.3496189 -0.3591711 -0.3673677 -0.3743715 -0.3803420 -0.3854358 -0.3898072 -0.3936091 -0.3969926 -0.4001082 -0.4031053 -0.4061325 -0.4093379 -0.4128594 -0.4167416 -0.4209756 -0.4255520 -0.4304610 -0.4356929 -0.4412381 -0.4470866 -0.4532286 -0.4596542 -0.4663535 -0.4733166 -0.4805335 -0.4879943 -0.4956893 -0.5036084 -0.5117418 -0.5200798 -0.5286126 -0.5373306 -0.5462241 -0.5552835 -0.5644995 -0.5738626 -0.5833635 -0.5929930 -0.6027420 -0.6126015 -0.6225627 -0.6326166 -0.6427547 -0.6529683 -0.6632491 -0.6735888 -0.6839790 -0.6944119 -0.7048793 -0.7153736 -0.7258870 -0.7364121 -0.7469413 -0.7574674 -0.7679833 -0.7784819 -0.7889564 -0.7993999 -0.8098059 -0.8201679
D3Ertd254e 2.6057166 2.4949461 2.3858907 2.2786514 2.1733226 2.0699916 1.9687397 1.8696416 1.7727668 1.6781788 1.5859362 1.4960929 1.4086979 1.3237964 1.2414296 1.1616353 1.0844481 1.0099001 0.9380205 0.8688367 0.8023743 0.7386576 0.6777097 0.6195530 0.5641859 0.5114928 0.4613285 0.4135543 0.3680374 0.3246505 0.2832716 0.2437830 0.2060718 0.1700290 0.1355494 0.1025312 0.0708761 0.0404887 0.0112762 -0.0168514 -0.0439816 -0.0701999 -0.0955894 -0.1202316 -0.1442059 -0.1675900 -0.1904600 -0.2128905 -0.2349546 -0.2567240 -0.2782688 -0.2996582 -0.3209558 -0.3421842 -0.3633430 -0.3844315 -0.4054489 -0.4263945 -0.4472676 -0.4680676 -0.4887939 -0.5094457 -0.5300226 -0.5505237 -0.5709486 -0.5912968 -0.6115675 -0.6317603 -0.6518746 -0.6719099 -0.6918657 -0.7117415 -0.7315369 -0.7512513 -0.7708843 -0.7904354 -0.8099043 -0.8292905 -0.8485935 -0.8678132 -0.8869489 -0.9060005 -0.9249674 -0.9438495 -0.9626463 -0.9813576 -0.9999830 -1.0185223 -1.0369752 -1.0553413 -1.0736205 -1.0918125 -1.1099171 -1.1279340 -1.1458630 -1.1637040 -1.1814567 -1.1991210 -1.2166966 -1.2341835
Ppara 2.7908849 2.6361951 2.4865194 2.3419331 2.2024874 2.0682113 1.9391147 1.8151896 1.6964129 1.5827483 1.4741479 1.3705544 1.2719029 1.1781222 1.0891367 1.0048678 0.9252352 0.8501580 0.7795566 0.7133531 0.6514729 0.5938455 0.5404057 0.4910944 0.4458174 0.4042874 0.3661794 0.3311921 0.2990457 0.2694788 0.2422467 0.2171188 0.1938772 0.1723149 0.1522347 0.1334477 0.1157724 0.0990342 0.0830639 0.0676978 0.0527767 0.0381460 0.0236551 0.0091574 -0.0054898 -0.0204253 -0.0357835 -0.0516947 -0.0682844 -0.0856731 -0.1039756 -0.1233010 -0.1437416 -0.1652873 -0.1878703 -0.2114219 -0.2358735 -0.2611563 -0.2872023 -0.3139440 -0.3413145 -0.3692484 -0.3976811 -0.4265498 -0.4557928 -0.4853505 -0.5151649 -0.5451798 -0.5753414 -0.6055975 -0.6358985 -0.6661965 -0.6964464 -0.7266050 -0.7566313 -0.7864870 -0.8161357 -0.8455435 -0.8746787 -0.9035116 -0.9320150 -0.9601637 -0.9879346 -1.0153065 -1.0422604 -1.0687791 -1.0948472 -1.1204511 -1.1455790 -1.1702206 -1.1943671 -1.2180115 -1.2411477 -1.2637715 -1.2858795 -1.3074696 -1.3285410 -1.3490936 -1.3691285 -1.3886477
D130040H23Rik 2.1775048 2.1049651 2.0337824 1.9639387 1.8954158 1.8281954 1.7622593 1.6975892 1.6341669 1.5719740 1.5109923 1.4512036 1.3925896 1.3351323 1.2788136 1.2236154 1.1695199 1.1165093 1.0645659 1.0136720 0.9638104 0.9149635 0.8671142 0.8202455 0.7743355 0.7293391 0.6852062 0.6418896 0.5993445 0.5575284 0.5164015 0.4759259 0.4360661 0.3967887 0.3580622 0.3198571 0.2821459 0.2449026 0.2081034 0.1717258 0.1357493 0.1001548 0.0649247 0.0300432 -0.0045042 -0.0387307 -0.0726480 -0.1062663 -0.1395948 -0.1726411 -0.2054120 -0.2379126 -0.2701457 -0.3020965 -0.3337418 -0.3650597 -0.3960298 -0.4266331 -0.4568519 -0.4866702 -0.5160729 -0.5450465 -0.5735787 -0.6016586 -0.6292761 -0.6564227 -0.6830908 -0.7092739 -0.7349667 -0.7601645 -0.7848641 -0.8090627 -0.8327588 -0.8559514 -0.8786406 -0.9008268 -0.9225116 -0.9436968 -0.9643853 -0.9845801 -1.0042851 -1.0235046 -1.0422432 -1.0605062 -1.0782991 -1.0956278 -1.1124987 -1.1289182 -1.1448933 -1.1604309 -1.1755384 -1.1902232 -1.2044931 -1.2183556 -1.2318189 -1.2448908 -1.2575794 -1.2698928 -1.2818392 -1.2934267
Otx1 2.0888985 2.0292717 1.9703747 1.9121830 1.8546731 1.7978223 1.7416087 1.6860114 1.6310102 1.5765855 1.5227188 1.4693921 1.4165882 1.3642907 1.3124836 1.2611519 1.2102811 1.1598575 1.1098677 1.0602992 1.0111401 0.9623789 0.9140049 0.8660078 0.8183824 0.7711454 0.7243192 0.6779247 0.6319820 0.5865096 0.5415251 0.4970448 0.4530842 0.4096574 0.3667775 0.3244569 0.2827068 0.2415373 0.2009580 0.1609772 0.1216027 0.0828414 0.0446993 0.0071818 -0.0297064 -0.0659613 -0.1015797 -0.1365588 -0.1708963 -0.2045907 -0.2376408 -0.2700460 -0.3018073 -0.3329368 -0.3634525 -0.3933721 -0.4227126 -0.4514905 -0.4797218 -0.5074221 -0.5346062 -0.5612889 -0.5874842 -0.6132059 -0.6384671 -0.6632808 -0.6876595 -0.7116152 -0.7351597 -0.7583045 -0.7810605 -0.8034386 -0.8254491 -0.8471021 -0.8684074 -0.8893745 -0.9100128 -0.9303311 -0.9503382 -0.9700424 -0.9894521 -1.0085752 -1.0274193 -1.0459921 -1.0643008 -1.0823524 -1.1001539 -1.1177119 -1.1350328 -1.1521231 -1.1689887 -1.1856357 -1.2020697 -1.2182963 -1.2343209 -1.2501489 -1.2657853 -1.2812351 -1.2965030 -1.3115938 
write.table(heatmap_matrix_q_value_0.01, file = file.path(tables_directory, "2-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6-significant_transcription_factors_diff_test_analysis_qval_0.01_heatmap_matrix.txt"), sep="\t", quote=FALSE, row.names=FALSE)
2.2.2.1.3 Plotting of transcription factors differentially expressed in pseudotime
2.2.2.1.3.1 Top 10 differentially expressed genes (q value < 5*10^-5)
transcription_factors_table_q_value_5_10_minus_5_ordered_qval <- arrange(transcription_factors_table_q_value_5_10_minus_5, qval)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[1]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[2]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[3]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[4]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[5]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[6]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[7]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[8]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[9]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[10]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

2.3 Selected genes

# Genes of interest.
genes_of_interest <- c("Aqp4", "Fabp7", "Kif9", "Mbp", "Nes", "Pdgfra", "Top2a")

# Remove genes of interest not present in Seurat dataset
genes_not_present <- genes_of_interest[!genes_of_interest %in% rownames(seurat@data)]
genes_of_interest <- genes_of_interest[!genes_of_interest %in% genes_not_present]
if(length(genes_not_present != 0)) {
  print(paste0("The following genes were not present in the Seurat object", genes_not_present))
}
      
diff_test_res <- differentialGeneTest(monocle[genes_of_interest],
      fullModelFormulaStr = "~sm.ns(Pseudotime)")
sig_gene_names <- row.names(subset(diff_test_res, qval < 0.1))
plot_pseudotime_heatmap(monocle[genes_of_interest,],
      num_clusters = 1,
      cores = 1,
      show_rownames = T)

2.3.1 Genes in pseudotime, single branch (Selected genes)

p <- plot_genes_in_pseudotime(monocle[genes_of_interest,], color_by="cluster") + scale_color_manual(values=colours)
p <- p %>% remove_geom("point")
p <- p %>% remove_geom("Line")
p <- p %>% + geom_line(aes(x = Pseudotime, y = expectation), size=1)
show(p)

2.3.2 Genes in pseudotime with branches (Selected genes)

p <- plot_genes_branched_pseudotime(monocle[genes_of_interest,], color_by="cluster") + scale_color_manual(values=colours)
show(p)

p <- p %>% remove_geom("point")
show(p)

3 Seurat tSNE plots

p <- cytokit::tsne(seurat, label=FALSE)
show(p)

p <- tsne_plot_clusters_highlighted(seurat, selected_clusters, legend=TRUE)
show(p)

p <- p + theme(legend.position = "none")
show(p)

p <- tsne_plot_clusters_highlighted_with_pseudotime(seurat, monocle, selected_clusters, legend=TRUE)
show(p)

p <- p + theme(legend.position = "none")
show(p)

4 Save monocle object to directory, and write pseudotime of cells to table.

save(monocle, file=file.path(monocle_objects_directory, "2-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6.Rda"))
cells_pseudotime <- pData(monocle) %>% select(cell, Pseudotime) %>% rename(pseudotime=Pseudotime)
write.table(cells_pseudotime, file.path(tables_directory, "2-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6_cell_pseudotime.txt"), sep="\t", quote=FALSE, row.names=FALSE)

5 Session info

sessionInfo()
## R version 3.5.0 (2018-04-23)
## Platform: x86_64-redhat-linux-gnu (64-bit)
## Running under: CentOS Linux 7 (Core)
## 
## Matrix products: default
## BLAS/LAPACK: /var/chroots/hydraex-centos-7/usr/lib64/R/lib/libRblas.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
##  [1] splines   stats4    parallel  stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] viridis_0.5.1       viridisLite_0.3.0   forcats_0.4.0      
##  [4] stringr_1.4.0       dplyr_0.8.0.1       purrr_0.3.0        
##  [7] tidyr_0.8.2         tibble_2.0.1        tidyverse_1.2.1    
## [10] Seurat_2.3.4        cowplot_0.9.4       R.utils_2.8.0      
## [13] R.oo_1.22.0         R.methodsS3_1.7.1   readr_1.3.1        
## [16] readxl_1.3.0        patchwork_0.0.1     monocle_2.10.1     
## [19] DDRTree_0.1.5       irlba_2.3.3         VGAM_1.1-1         
## [22] Biobase_2.42.0      BiocGenerics_0.28.0 Matrix_1.2-15      
## [25] kableExtra_1.0.1    ggedit_0.3.0        ggplot2_3.1.0      
## [28] cytokit_0.6.0       pheatmap_1.0.12     colorRamps_2.3     
## 
## loaded via a namespace (and not attached):
##   [1] snow_0.4-3           backports_1.1.3      Hmisc_4.2-0         
##   [4] plyr_1.8.4           igraph_1.2.4         lazyeval_0.2.1      
##   [7] densityClust_0.3     fastICA_1.2-1        digest_0.6.18       
##  [10] foreach_1.4.4        htmltools_0.3.6      lars_1.2            
##  [13] gdata_2.18.0         magrittr_1.5         checkmate_1.9.1     
##  [16] cluster_2.0.7-1      mixtools_1.1.0       ROCR_1.0-7          
##  [19] limma_3.38.3         modelr_0.1.3         matrixStats_0.54.0  
##  [22] docopt_0.6.1         colorspace_1.4-0     ggrepel_0.8.0       
##  [25] rvest_0.3.2          haven_2.0.0          xfun_0.4            
##  [28] sparsesvd_0.1-4      crayon_1.3.4         jsonlite_1.6        
##  [31] survival_2.43-3      zoo_1.8-4            iterators_1.0.10    
##  [34] ape_5.2              glue_1.3.0           gtable_0.2.0        
##  [37] webshot_0.5.1        kernlab_0.9-27       prabclus_2.2-7      
##  [40] DEoptimR_1.0-8       scales_1.0.0         mvtnorm_1.0-8       
##  [43] bibtex_0.4.2         miniUI_0.1.1.1       Rcpp_1.0.0          
##  [46] metap_1.1            dtw_1.20-1           xtable_1.8-3        
##  [49] htmlTable_1.13.1     reticulate_1.11.1    foreign_0.8-71      
##  [52] bit_1.1-14           proxy_0.4-22         mclust_5.4.2        
##  [55] SDMTools_1.1-221     Formula_1.2-3        tsne_0.1-3          
##  [58] htmlwidgets_1.3      httr_1.4.0           FNN_1.1.3           
##  [61] gplots_3.0.1.1       RColorBrewer_1.1-2   shinyAce_0.3.3      
##  [64] fpc_2.1-11.1         acepack_1.4.1        modeltools_0.2-22   
##  [67] ica_1.0-2            pkgconfig_2.0.2      flexmix_2.3-14      
##  [70] nnet_7.3-12          labeling_0.3         tidyselect_0.2.5    
##  [73] rlang_0.3.1          reshape2_1.4.3       later_0.8.0         
##  [76] cellranger_1.1.0     munsell_0.5.0        tools_3.5.0         
##  [79] cli_1.0.1            generics_0.0.2       broom_0.5.1         
##  [82] ggridges_0.5.1       evaluate_0.13        shinyBS_0.61        
##  [85] yaml_2.2.0           npsurv_0.4-0         knitr_1.21          
##  [88] bit64_0.9-7          fitdistrplus_1.0-14  robustbase_0.93-3   
##  [91] caTools_1.17.1.1     randomForest_4.6-14  RANN_2.6.1          
##  [94] pbapply_1.4-0        nlme_3.1-137         mime_0.6            
##  [97] slam_0.1-44          xml2_1.2.0           hdf5r_1.0.0         
## [100] compiler_3.5.0       rstudioapi_0.9.0     png_0.1-7           
## [103] lsei_1.2-0           stringi_1.3.1        highr_0.7           
## [106] lattice_0.20-35      trimcluster_0.1-2.1  HSMMSingleCell_1.2.0
## [109] pillar_1.3.1         combinat_0.0-8       Rdpack_0.10-1       
## [112] lmtest_0.9-36        data.table_1.12.0    bitops_1.0-6        
## [115] gbRd_0.4-11          httpuv_1.4.5.1       R6_2.4.0            
## [118] latticeExtra_0.6-28  promises_1.0.1       KernSmooth_2.23-15  
## [121] gridExtra_2.3        codetools_0.2-15     MASS_7.3-51.1       
## [124] gtools_3.8.1         assertthat_0.2.0     withr_2.1.2         
## [127] qlcMatrix_0.9.7      diptest_0.75-7       doSNOW_1.0.16       
## [130] hms_0.4.2            grid_3.5.0           rpart_4.1-13        
## [133] class_7.3-14         rmarkdown_1.11       segmented_0.5-3.0   
## [136] Rtsne_0.15           lubridate_1.7.4      shiny_1.2.0         
## [139] base64enc_0.1-3